Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_028485576.1 B076_RS0100465 homoserine kinase
Query= curated2:Q9RAM6 (319 letters) >NCBI__GCF_000483485.1:WP_028485576.1 Length = 317 Score = 291 bits (745), Expect = 1e-83 Identities = 148/310 (47%), Positives = 199/310 (64%), Gaps = 9/310 (2%) Query: 1 MSVFTTVSFEQMQQWLKGYDLGELLDLQGIASGITNTNYFVTTD-NG---RYVLTLFEEH 56 MSV+T V Q+ ++LK Y++G L +GI++GI NTNYFV T+ NG R+VLT+FE H Sbjct: 1 MSVYTVVDEPQLIEFLKDYEVGSLKSFEGISAGIENTNYFVDTNLNGETKRFVLTIFEHH 60 Query: 57 SAEELPNFLDLMTHLAERGIPCPHPVKNNAGRALGELNGKPAALVSCLAGRSLDNPMPQH 116 S EELP FLD+M +AE IP HP++ + L EL GKPAALV L G +++P Sbjct: 61 SFEELPYFLDIMAFMAEHQIPTAHPIQTLSNGYLKELYGKPAALVERLTGSGVEDPSEIQ 120 Query: 117 CAAIGEVLARMHIAGASFKAGMSNLRGQEWRIATAAKVAPFLDEENHRMLDAQLEFERTF 176 C +GE LAR H AGA F++ +N R +W AT ++ FL ++ +M+ +L F+ T Sbjct: 121 CGVMGEQLARFHQAGAGFESKRTNDRDLQWMQATFKQIEAFLPDDEKQMITQELAFQSTI 180 Query: 177 DTRRLPRGVIHADLFRDNVLMDGDKVGGVIDFYYACHDALLYDIAIAVNDWC-----VNA 231 D LP+GVIHADLF DN L DGD++ G+ID YYAC+ LYD+A+ VNDWC Sbjct: 181 DWAHLPQGVIHADLFCDNALFDGDQLSGIIDLYYACNSTFLYDLAVMVNDWCRLHSEQPL 240 Query: 232 DCTLDAVRVRAFLDAYHAIRPLTGEEHAAWPGMLRVAAMRFWLSRLNDLYFPQAGELTHA 291 + D +V A + Y RPLT E AWP LR+AA+RF+LSRL DL+ P+ GE+T Sbjct: 241 EIHFDQAKVEAMVSTYQKQRPLTDAEQKAWPAALRLAALRFFLSRLKDLHIPREGEMTQI 300 Query: 292 KDPAYFERIL 301 KDP F+R+L Sbjct: 301 KDPKVFKRVL 310 Lambda K H 0.324 0.137 0.430 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 296 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 319 Length of database: 317 Length adjustment: 27 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 bits)
Align candidate WP_028485576.1 B076_RS0100465 (homoserine kinase)
to HMM TIGR00938 (thrB: homoserine kinase (EC 2.7.1.39))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00938.hmm # target sequence database: /tmp/gapView.19584.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00938 [M=307] Accession: TIGR00938 Description: thrB_alt: homoserine kinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-104 333.5 0.0 7.1e-104 333.4 0.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028485576.1 B076_RS0100465 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028485576.1 B076_RS0100465 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.4 0.0 7.1e-104 7.1e-104 1 306 [. 1 311 [. 1 312 [. 0.95 Alignments for each domain: == domain 1 score: 333.4 bits; conditional E-value: 7.1e-104 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnylltt....dkgryvLtlyekrvkaeeLPff 65 m+vyt v + +l +fL+ y++G l s++Gi+ G+en+ny+++t +++r+vLt++e+++ eeLP+f lcl|NCBI__GCF_000483485.1:WP_028485576.1 1 MSVYTVVDEPQLIEFLKDYEVGSLKSFEGISAGIENTNYFVDTnlngETKRFVLTIFEHHS-FEELPYF 68 9****************************************994444578***********.******* PP TIGR00938 66 lellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagad 134 l+++ ++ae+ +p+a+p+++ + l+eL GkPaalve L+Gs v+ P +c +ge la++h aga+ lcl|NCBI__GCF_000483485.1:WP_028485576.1 69 LDIMAFMAEHQIPTAHPIQTLSNGYLKELYGKPAALVERLTGSGVEDPSEIQCGVMGEQLARFHQAGAG 137 ********************************************************************* PP TIGR00938 135 fkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldg 203 f+++r+nd r +W ++ k+ + +l +++++++++el++ ++++ +LP+gvihadlf dn l+dg lcl|NCBI__GCF_000483485.1:WP_028485576.1 138 FESKRTND-RDLQWMQATFKQ--IEAFLPDDEKQMITQELAFQSTIDWAHLPQGVIHADLFCDNALFDG 203 *******6.556799999999..8889****************************************** PP TIGR00938 204 dklkgvidfyfaCedallydlaiavndWcfea.....ddkldaaaakallkgyeavrpLseeekaafpv 267 d+l+g+id+y+aC+ ++lydla+ vndWc+ + ++d+a++ a++ +y+++rpL++ e++a+p lcl|NCBI__GCF_000483485.1:WP_028485576.1 204 DQLSGIIDLYYACNSTFLYDLAVMVNDWCRLHseqplEIHFDQAKVEAMVSTYQKQRPLTDAEQKAWPA 272 *****************************854122335699**************************** PP TIGR00938 268 llrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +lr aalrf+lsrl+dl+ ++ ge++++kdP+ f+r L+ lcl|NCBI__GCF_000483485.1:WP_028485576.1 273 ALRLAALRFFLSRLKDLHIPREGEMTQIKDPKVFKRVLA 311 ************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (317 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.48 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory